Five Thousand New Genes in the Honey Bee Genome

Originally published in 2006, as one of the early draft genome sequences, the Honey Bee genome has served the research community well.  We have revisited this genome, adding new whole genome sequence to improve the contiguity of the genome and using additional mRNA sequence and comparative data and more modern gene annotation methods to improve the gene annotations.  The combinations of these efforts has increased the contig N50 from 41 to 45 kb, increased the scaffold N50 from 362 to 997 kb, anchored an additional 5.5% of the genome to chromosomes and identified ~5,000 new genes.  Many of the new protein coding genes are single exon genes and are less likely to have a protein homolog than previously known genes.  Gene ontology analysis showed that the new genes are enriched for the biological functions “apoptosis”, “neurotransmitter release” and “secondary active organic cation transmembrane transporter”.  Proportionally more genes with Interpro domains of “Transposase, type 1” and “Olfactory receptor, Drosophila” are included in the new OGSv3.2 gene set as well.  New genes are less likely to be broadly expressed compared to previously known genes, although most (>54%) have some transcript evidence.  In total, 92 % of the genes have supporting biological evidence from transcript sequence, peptide sequence, protein homolog or Interpro domains, including comparative sequence from other bees increases this fraction of genes with biological evidence to 96%.